Then the problem isn't the fd leaking, the problem is that the fd is being closed twice. If SQLite owns that fd then it's obviously no longer owned by the Named

Then the problem isn't the fd leaking, the problem is that the fd is being closed twice. If SQLite owns that fd then it's obviously no longer owned by the NamedTemporaryFile, so something closed it. So either NamedTemporaryFile is closing an underlying fd twice (that sounds like a horrible Python bug, it should never be allowed) or some piece of code somewhere did one of those horrible "close all fds from 3 to 1024" things at one point, and SQLite then reused an fd that was still assigned to a live File object.